Kate Culhane, Dept. of Ecology, Evolution, and Marine Biology, UC Santa Barbara
kathrynculhane@ucsb.edu
Summary
Wrangling data
DEPENDENCIES
##### PACKAGES #####
library(tidyverse) # data manipulation & visualization
library(lubridate) # wrangling dates
##### DATA #####
# Stomach pump invert ID (all islands)
diet_raw <- read_csv('data_raw/field/diet_field.csv')
# Site metadata (Naxos)
meta_raw <- read_csv('data_raw/field/naxos_meta.csv')
# Vegetation quadrats (Naxos)
veg_raw <- read_csv('data_raw/field/naxos_veg.csv')
# Pitfall/sticky metadata (all islands)
prey_meta_raw <- read_csv('data_raw/field/prey_meta.csv',
col_types = "??cccc???????????????")
# Pitfall trap invert ID (all islands)
prey_p_raw <- read_csv('data_raw/field/prey_pitfall.csv')
# Sticky trap invert ID (all islands)
prey_s_raw <- read_csv('data_raw/field/prey_sticky.csv')OUTPUT FILES
# Trap metadata
trap_veg <- prey_meta_raw %>%
filter(island == "Naxos") %>%
select(2, 8, 11:21)
write_csv(trap_veg, "output/02_trap_veg.csv", col_names = TRUE)
trap_veg# Trap metadata
prey_meta <- prey_meta_raw %>%
filter(island == "Naxos") %>%
left_join(prey_p_raw[c(2,4,31)], by = c("site", "trap")) %>%
left_join(prey_s_raw[c(2,4,24)], by = c("site", "trap")) %>%
mutate(comments_p = comments.y,
comments_s = comments,
comments = comments.x,
set = dmy_hm(paste(date_set, time_set)),
collected = dmy_hm(paste(date_coll, time_coll)),
hours_open = as.numeric(collected - set)*24,
pitfall_effort = case_when(
pitfall_condition == "GOOD" ~ 1,
pitfall_condition == "FLAW" ~ 0.5,
pitfall_condition == "LOST" ~ 0),
sticky_effort = case_when(
sticky_condition == "GOOD" ~ 1,
sticky_condition == "FLAW" ~ 0.5,
sticky_condition == "LOST" ~ 0
)) %>%
select(site, set, collected, hours_open, crew, trap,
pitfall_condition, pitfall_effort, sticky_condition, sticky_effort,
comments, comments_p, comments_s)
write_csv(prey_meta, "output/02_prey_meta.csv", col_names = TRUE)
prey_meta# Pitfall trap data
prey_p <- prey_p_raw %>%
filter(island == "Naxos") %>%
mutate(trap_type = "pitfall",
sample = paste0(site, "-P", trap)) %>%
select(-gecko, -lizard) %>% # remove columns for non-invertebrates
pivot_longer(5:28, names_to = "order", values_to = "count")
# Sticky trap data
prey_s <- prey_s_raw %>%
filter(island == "Naxos") %>%
mutate(trap_type = "sticky",
sample = paste0(site, "-S", trap)) %>%
select(-gecko) %>% # remove columns for non-invertebrates
pivot_longer(5:22, names_to = "order", values_to = "count")
# All trap data
prey <- full_join(prey_p, prey_s) %>%
filter(count != 0) %>%
select(sample, site, trap, trap_type, order, count)
write_csv(prey, "output/02_prey.csv", col_names = TRUE)
preyprey_matrix <- prey %>%
pivot_wider(names_from = order, values_from = count) %>%
replace(., is.na(.), 0)
write_csv(prey_matrix, "output/02_prey_matrix.csv", col_names = TRUE)
prey_matrixdiet_inverts <- diet_raw %>%
filter(island == "Naxos") %>%
select(-c(1, 33:43)) %>%
pivot_longer(4:31, names_to = "order", values_to = "count") %>%
filter(count != 0)
write_csv(diet_inverts, "output/02_diet_inverts.csv", col_names = TRUE)
diet_invertsdiet_matrix <- diet_inverts %>%
select(-date, -comments) %>%
pivot_wider(names_from = order, values_from = count) %>%
replace(., is.na(.), 0)
write_csv(diet_matrix, "output/02_diet_matrix.csv", col_names = TRUE)
diet_matrixdiet_veg <- diet_raw %>%
filter(island == "Naxos") %>%
select(-c(5:32)) %>%
pivot_longer(5:15, names_to = "order", values_to = "count") %>%
filter(count != 0)
write_csv(diet_veg, "output/02_diet_veg.csv", col_names = TRUE)
diet_veg
devtools::session_info()## - Session info ------------------------------------------------------------------------------------------
## setting value
## version R version 4.1.0 (2021-05-18)
## os Windows 10 x64
## system i386, mingw32
## ui RStudio
## language (EN)
## collate English_United States.1252
## ctype English_United States.1252
## tz America/Los_Angeles
## date 2021-07-27
##
## - Packages ----------------------------------------------------------------------------------------------
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## [2] C:/Users/kathr/AppData/Local/Temp/RtmpWykWok/renv-system-library
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